Xampp for Linux comes with hardcoded pathnames, but via symbolic link you could run several installations. Anyway, running more than one installation is a waste of ressources, its quite easy and sophisticated to use virtualhosts for different projects, i.e for different PHP versions. You then might use as many PHP versions at the same time, what does not work if you use the cludgy solution by using two or more installations.

Therefore i cannot see any real disadvantage with hard coded pathnames, its all a question of an intelligently designed configuration.